Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold260
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1006324
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
File 7 of 7
Found at i:944741 original size:14 final size:14
Alignment explanation
Indices: 944722--944783 Score: 53
Period size: 14 Copynumber: 4.6 Consensus size: 14
944712 TTAATAATTT
944722 TAAATATAACTATA
1 TAAATATAACTATA
944736 TAAATA-AA-TATA
1 TAAATATAACTATA
944748 -AAATAAATAAC-ATA
1 TAAAT--ATAACTATA
*
944762 TTAAATAT-ACGATA
1 -TAAATATAACTATA
944776 TAAATATA
1 TAAATATA
944784 TATTTTAAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 16
0.71 0.00 0.29
Matches are distributed among these distances:
11 4 0.10
12 4 0.10
13 12 0.30
14 16 0.40
16 4 0.10
ACGTcount: A:0.61, C:0.05, G:0.02, T:0.32
Consensus pattern (14 bp):
TAAATATAACTATA
Found at i:944767 original size:16 final size:15
Alignment explanation
Indices: 944735--944768 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
944725 ATATAACTAT
944735 ATAAATAAATATAAA
1 ATAAATAAATATAAA
*
944750 ATAAATAACATATTAA
1 ATAAATAA-ATATAAA
944766 ATA
1 ATA
944769 TACGATATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (15 bp):
ATAAATAAATATAAA
Found at i:944781 original size:13 final size:12
Alignment explanation
Indices: 944725--944783 Score: 50
Period size: 12 Copynumber: 4.9 Consensus size: 12
944715 ATAATTTTAA
* *
944725 ATATAACTATAT
1 ATATAAATATAC
*
944737 AAATAAATATA-
1 ATATAAATATAC
*
944748 AAATAAATA-AC
1 ATATAAATATAC
944759 ATATTAAATATAC
1 ATA-TAAATATAC
944772 GATATAAATATA
1 -ATATAAATATA
944784 TATTTTAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
10 1 0.03
11 11 0.28
12 15 0.38
13 10 0.25
14 3 0.08
ACGTcount: A:0.61, C:0.05, G:0.02, T:0.32
Consensus pattern (12 bp):
ATATAAATATAC
Found at i:945356 original size:22 final size:20
Alignment explanation
Indices: 945330--945387 Score: 57
Period size: 18 Copynumber: 2.9 Consensus size: 20
945320 TTCGTTTAAA
945330 TTTATTTATATTATAAATATTT
1 TTTATTTAT-TT-TAAATATTT
945352 TTTA-TT-TTTTAAATATTT
1 TTTATTTATTTTAAATATTT
* *
945370 TTAATTTAATTTTTAATA
1 TTTATTT-ATTTTAAATA
945388 ATTAAATATA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
18 12 0.39
19 4 0.13
20 1 0.03
21 10 0.32
22 4 0.13
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (20 bp):
TTTATTTATTTTAAATATTT
Found at i:945364 original size:18 final size:18
Alignment explanation
Indices: 945324--945376 Score: 63
Period size: 18 Copynumber: 3.0 Consensus size: 18
945314 TTTAAGTTCG
* *
945324 TTTAAAT-TTATTTATAT
1 TTTAAATATTTTTTATTT
*
945341 TATAAATATTTTTTATTT
1 TTTAAATATTTTTTATTT
*
945359 TTTAAATATTTTTAATTT
1 TTTAAATATTTTTTATTT
945377 AATTTTTAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
17 6 0.20
18 24 0.80
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (18 bp):
TTTAAATATTTTTTATTT
Found at i:945404 original size:15 final size:14
Alignment explanation
Indices: 945360--945407 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 14
945350 TTTTTATTTT
945360 TTAAATATTTTTAA
1 TTAAATATTTTTAA
*
945374 TTTAAT-TTTTAATAA
1 TTAAATATTTT--TAA
945389 TTAAATATATTTTAA
1 TTAAATAT-TTTTAA
945404 TTAA
1 TTAA
945408 GTTTTTTTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
13 4 0.14
14 5 0.18
15 15 0.54
16 1 0.04
17 3 0.11
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
TTAAATATTTTTAA
Found at i:946596 original size:3 final size:3
Alignment explanation
Indices: 946583--946614 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
946573 TATGTTTTAT
946583 TTA TT- TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
946615 CCTTTCATGC
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 26 0.93
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:946836 original size:22 final size:22
Alignment explanation
Indices: 946795--946837 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
946785 TTAAATAATT
* **
946795 TATAAAGTATGATTTTTTTTTA
1 TATAAAGTATGAATGGTTTTTA
946817 TATAAAGTATGAATGGTTTTT
1 TATAAAGTATGAATGGTTTTT
946838 GACCATTGTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.14, T:0.53
Consensus pattern (22 bp):
TATAAAGTATGAATGGTTTTTA
Found at i:947808 original size:2 final size:2
Alignment explanation
Indices: 947752--947788 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
947742 AATTGTTATG
*
947752 TA TA -A TA TA TA TA TA TT TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
947789 CACACACATA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:949797 original size:28 final size:28
Alignment explanation
Indices: 949760--949824 Score: 75
Period size: 26 Copynumber: 2.4 Consensus size: 28
949750 ATTCAATTTT
949760 TATA-TTAAATTATCTATATTATTT-TATA
1 TATATTTAAATTAT-TATA-TATTTATATA
*
949788 TAT-TTTAAA-TATTATATATTTATATT
1 TATATTTAAATTATTATATATTTATATA
949814 TATATTTAAAT
1 TATATTTAAAT
949825 ATATATTAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
25 5 0.16
26 10 0.31
27 9 0.28
28 8 0.25
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (28 bp):
TATATTTAAATTATTATATATTTATATA
Found at i:949804 original size:16 final size:15
Alignment explanation
Indices: 949783--949830 Score: 59
Period size: 12 Copynumber: 3.4 Consensus size: 15
949773 CTATATTATT
949783 TTATATATTTTAAATA
1 TTATATA-TTTAAATA
949799 TTATATATTT--ATA
1 TTATATATTTAAATA
949812 TT-TATATTTAAATA
1 TTATATATTTAAATA
949826 -TATAT
1 TTATAT
949831 TAAACATAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
12 7 0.24
13 6 0.21
14 6 0.21
15 3 0.10
16 7 0.24
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
TTATATATTTAAATA
Found at i:956739 original size:16 final size:16
Alignment explanation
Indices: 956699--956745 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
956689 ATAACTCTCT
*
956699 TTTTCAGAAAAATTTA
1 TTTTCAAAAAAATTTA
*
956715 TCTAT-AAAAAAATTTA
1 T-TTTCAAAAAAATTTA
*
956731 TTTTCAAAATAATTT
1 TTTTCAAAAAAATTT
956746 CATAGAACAA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
15 2 0.08
16 21 0.84
17 2 0.08
ACGTcount: A:0.47, C:0.06, G:0.02, T:0.45
Consensus pattern (16 bp):
TTTTCAAAAAAATTTA
Found at i:957917 original size:27 final size:27
Alignment explanation
Indices: 957871--957924 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
957861 TTTAATTTTA
957871 ATTTCAAGAAAATCTAAAAAAAATAAT
1 ATTTCAAGAAAATCTAAAAAAAATAAT
*
957898 ATTTCAA-AAAATCTTTAAAAAAATAAT
1 ATTTCAAGAAAATC-TAAAAAAAATAAT
957925 TAAAAAAAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 6 0.24
27 19 0.76
ACGTcount: A:0.61, C:0.07, G:0.02, T:0.30
Consensus pattern (27 bp):
ATTTCAAGAAAATCTAAAAAAAATAAT
Found at i:957920 original size:12 final size:12
Alignment explanation
Indices: 957889--957932 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
957879 AAAATCTAAA
957889 AAAAATAATATTT
1 AAAAA-AATATTT
* *
957902 CAAAAAATCTTT
1 AAAAAAATATTT
*
957914 AAAAAAATAATT
1 AAAAAAATATTT
957926 AAAAAAA
1 AAAAAAA
957933 AGAATAAGTT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
12 22 0.85
13 4 0.15
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.27
Consensus pattern (12 bp):
AAAAAAATATTT
Found at i:962895 original size:20 final size:20
Alignment explanation
Indices: 962870--962908 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
962860 TTATAATGTC
**
962870 AACAAAATTTAGCATCATAT
1 AACAAAATCAAGCATCATAT
962890 AACAAAATCAAGCATCATA
1 AACAAAATCAAGCATCATA
962909 CCTCGATATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.54, C:0.18, G:0.05, T:0.23
Consensus pattern (20 bp):
AACAAAATCAAGCATCATAT
Found at i:963110 original size:21 final size:20
Alignment explanation
Indices: 963067--963111 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 20
963057 TTTTGCTTGT
*
963067 TGTTGCTTGTTTGCTGCTGG
1 TGTTGCTTGGTTGCTGCTGG
* *
963087 TGTTGCTTCGGTTGTTGTTGG
1 TGTTGCTT-GGTTGCTGCTGG
963108 TGTT
1 TGTT
963112 ACTGCTAGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 8 0.38
21 13 0.62
ACGTcount: A:0.00, C:0.11, G:0.36, T:0.53
Consensus pattern (20 bp):
TGTTGCTTGGTTGCTGCTGG
Found at i:963230 original size:24 final size:23
Alignment explanation
Indices: 963190--963235 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
963180 TATTTCGTTT
*
963190 CTGTTTTGTTTCTTTTTGTTTCTG
1 CTGTTTTCTTTCTTTTT-TTTCTG
963214 CTGTTTTCTTT-TATTTTTTTCT
1 CTGTTTTCTTTCT-TTTTTTTCT
963236 TCCTATTCGA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 6 0.30
24 14 0.70
ACGTcount: A:0.02, C:0.13, G:0.11, T:0.74
Consensus pattern (23 bp):
CTGTTTTCTTTCTTTTTTTTCTG
Found at i:963541 original size:20 final size:20
Alignment explanation
Indices: 963508--963556 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
963498 TATTAAGATC
* *
963508 ATATAAATAAACACATATAT
1 ATATATATACACACATATAT
*
963528 GTATATATACACACATATAT
1 ATATATATACACACATATAT
963548 ATATATATA
1 ATATATATA
963557 TATATTTATA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.53, C:0.10, G:0.02, T:0.35
Consensus pattern (20 bp):
ATATATATACACACATATAT
Found at i:963545 original size:18 final size:18
Alignment explanation
Indices: 963508--963554 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
963498 TATTAAGATC
* * *
963508 ATATAAATAAACACATAT
1 ATATATATATACACACAT
*
963526 ATGTATATATACACACAT
1 ATATATATATACACACAT
963544 ATATATATATA
1 ATATATATATA
963555 TATATATTTA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.53, C:0.11, G:0.02, T:0.34
Consensus pattern (18 bp):
ATATATATATACACACAT
Found at i:964162 original size:20 final size:20
Alignment explanation
Indices: 964133--964170 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
964123 TTACTAAAAC
964133 TTTTACGTAACAATATTAAG
1 TTTTACGTAACAATATTAAG
* *
964153 TTTTATGTAATAATATTA
1 TTTTACGTAACAATATTA
964171 TTATGATTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.39, C:0.05, G:0.08, T:0.47
Consensus pattern (20 bp):
TTTTACGTAACAATATTAAG
Found at i:965340 original size:24 final size:24
Alignment explanation
Indices: 965313--965360 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
965303 TATTTTCATA
*
965313 TAATT-TTTTTGTTATATTATATTT
1 TAATTATTTTT-TCATATTATATTT
965337 TAATTATTTTTTCATATTATATTT
1 TAATTATTTTTTCATATTATATTT
965361 GTGTGTAACG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 17 0.77
25 5 0.23
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.69
Consensus pattern (24 bp):
TAATTATTTTTTCATATTATATTT
Found at i:969039 original size:25 final size:26
Alignment explanation
Indices: 969004--969058 Score: 85
Period size: 25 Copynumber: 2.2 Consensus size: 26
968994 AACGGACTTC
*
969004 AAAGTATATGAACGATGCACCCTTGG
1 AAAGTATATGAACGATACACCCTTGG
*
969030 AAAG-ATATGAATGATACACCCTTGG
1 AAAGTATATGAACGATACACCCTTGG
969055 AAAG
1 AAAG
969059 CTAACATAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
25 23 0.85
26 4 0.15
ACGTcount: A:0.40, C:0.16, G:0.22, T:0.22
Consensus pattern (26 bp):
AAAGTATATGAACGATACACCCTTGG
Found at i:969712 original size:49 final size:49
Alignment explanation
Indices: 969624--969727 Score: 117
Period size: 49 Copynumber: 2.1 Consensus size: 49
969614 AACTCATTTA
* *
969624 TTTATATTATATTTATATATTTTACTTATCATAATTATATT-TAAAATAT
1 TTTATATTATATTTATATATTTTAATTATAATAATTATATTATAAAA-AT
*
969673 TTTATATT-TATTTA-A-ATTTTAATATATTAATAATTTATATTATATAAAT
1 TTTATATTATATTTATATATTTTAAT-TA-TAATAA-TTATATTATAAAAAT
969722 TTTATA
1 TTTATA
969728 CATATATTAA
Statistics
Matches: 48, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
46 7 0.15
47 3 0.06
48 11 0.23
49 23 0.48
50 4 0.08
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (49 bp):
TTTATATTATATTTATATATTTTAATTATAATAATTATATTATAAAAAT
Found at i:969724 original size:32 final size:36
Alignment explanation
Indices: 969668--969772 Score: 105
Period size: 37 Copynumber: 3.0 Consensus size: 36
969658 TTATATTTAA
* *
969668 AATATTTTATATTTATTTAAA-TTT-TA-ATATATT
1 AATAATTTATATTTATATAAATTTTATACATATATT
969701 AATAATTTATA-TTATATAAATTTTATACATATATT
1 AATAATTTATATTTATATAAATTTTATACATATATT
* *
969736 AAT-ATTGTATCATGTATTTAATATTTT-TACATATATT
1 AATAATT-TAT-ATTTATATAA-ATTTTATACATATATT
969773 GTATTTATAT
Statistics
Matches: 61, Mismatches: 4, Indels: 10
0.81 0.05 0.13
Matches are distributed among these distances:
32 8 0.13
33 13 0.21
34 5 0.08
35 13 0.21
36 1 0.02
37 16 0.26
38 5 0.08
ACGTcount: A:0.40, C:0.03, G:0.02, T:0.55
Consensus pattern (36 bp):
AATAATTTATATTTATATAAATTTTATACATATATT
Found at i:969725 original size:16 final size:17
Alignment explanation
Indices: 969658--969762 Score: 67
Period size: 16 Copynumber: 6.1 Consensus size: 17
969648 CTTATCATAA
*
969658 TTATATT-TAAAATATT
1 TTATATTATATAATATT
*
969674 TTATATTTATTTAA-ATT
1 TTATA-TTATATAATATT
*
969691 TTA-A-TATATTAATAAT
1 TTATATTATA-TAATATT
969707 TTATATTATATAA-ATT
1 TTATATTATATAATATT
*
969723 TTATACATATATTAATATT
1 TTATA-TTATA-TAATATT
* *
969742 GTATCATGTATTTAATATT
1 TTAT-AT-TATATAATATT
969761 TT
1 TT
969763 TACATATATT
Statistics
Matches: 68, Mismatches: 10, Indels: 19
0.70 0.10 0.20
Matches are distributed among these distances:
14 3 0.04
15 3 0.04
16 18 0.26
17 16 0.24
18 10 0.15
19 14 0.21
20 4 0.06
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (17 bp):
TTATATTATATAATATT
Found at i:971434 original size:13 final size:13
Alignment explanation
Indices: 971416--971440 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
971406 ATTTTGCTTA
971416 GTATCGATACATT
1 GTATCGATACATT
971429 GTATCGATACAT
1 GTATCGATACAT
971441 AAAACTGGCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:971559 original size:42 final size:41
Alignment explanation
Indices: 971494--971572 Score: 113
Period size: 42 Copynumber: 1.9 Consensus size: 41
971484 TTTATCACTA
* *
971494 TTCATGTATCGATGCATTGTGAATAGTATCGATACATTACTG
1 TTCATGTATCGATACATTATGAATAGT-TCGATACATTACTG
* *
971536 TTCATGTATTGATATATTATGAATAGTTCGATACATT
1 TTCATGTATCGATACATTATGAATAGTTCGATACATT
971573 GAGTCTAACG
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
41 10 0.30
42 23 0.70
ACGTcount: A:0.30, C:0.11, G:0.16, T:0.42
Consensus pattern (41 bp):
TTCATGTATCGATACATTATGAATAGTTCGATACATTACTG
Found at i:973658 original size:21 final size:21
Alignment explanation
Indices: 973634--973692 Score: 82
Period size: 21 Copynumber: 2.8 Consensus size: 21
973624 TAATATTCTT
* *
973634 GAAAAGAAATTAAGTGAATTA
1 GAAAAGAAAATAAATGAATTA
973655 GAAAAGAAAATAAATGAATTA
1 GAAAAGAAAATAAATGAATTA
* *
973676 GAAGAGAAAAGAAATGA
1 GAAAAGAAAATAAATGA
973693 GTTGCAAGTG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.63, C:0.00, G:0.20, T:0.17
Consensus pattern (21 bp):
GAAAAGAAAATAAATGAATTA
Found at i:976253 original size:15 final size:15
Alignment explanation
Indices: 976233--976265 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
976223 ATGAGAGTTC
976233 ATAAAAAGGGAGAGA
1 ATAAAAAGGGAGAGA
976248 ATAAAAAGGGAGAGA
1 ATAAAAAGGGAGAGA
976263 ATA
1 ATA
976266 GATTTGGCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.61, C:0.00, G:0.30, T:0.09
Consensus pattern (15 bp):
ATAAAAAGGGAGAGA
Found at i:976941 original size:21 final size:21
Alignment explanation
Indices: 976899--976942 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
976889 GATATGATTA
*
976899 AATGTTTTTCAAGCAAAGAAAT
1 AATGTTTTTCAA-CAAAAAAAT
976921 AATGTTTTTCAA-AATAAAAAT
1 AATGTTTTTCAACAA-AAAAAT
976942 A
1 A
976943 CGTGATGTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 2 0.10
21 6 0.30
22 12 0.60
ACGTcount: A:0.50, C:0.07, G:0.09, T:0.34
Consensus pattern (21 bp):
AATGTTTTTCAACAAAAAAAT
Found at i:977129 original size:10 final size:10
Alignment explanation
Indices: 977114--977148 Score: 70
Period size: 10 Copynumber: 3.5 Consensus size: 10
977104 ATCTCATTTT
977114 TCACTGTTCA
1 TCACTGTTCA
977124 TCACTGTTCA
1 TCACTGTTCA
977134 TCACTGTTCA
1 TCACTGTTCA
977144 TCACT
1 TCACT
977149 ATTAATGTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.20, C:0.31, G:0.09, T:0.40
Consensus pattern (10 bp):
TCACTGTTCA
Found at i:977201 original size:42 final size:41
Alignment explanation
Indices: 977142--977227 Score: 127
Period size: 42 Copynumber: 2.1 Consensus size: 41
977132 CATCACTGTT
977142 CATCACTATTAATGTATCGATACATTGTGAATAGTATCAATA
1 CATCACTATTAATGTATCGATACATTGTGAATAGT-TCAATA
* * * *
977184 CATCACTGTTTATGTATCGATATATTGTGAATAGTTCGATA
1 CATCACTATTAATGTATCGATACATTGTGAATAGTTCAATA
977225 CAT
1 CAT
977228 TGAGTCCAAC
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
41 8 0.20
42 32 0.80
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.38
Consensus pattern (41 bp):
CATCACTATTAATGTATCGATACATTGTGAATAGTTCAATA
Found at i:978417 original size:3 final size:3
Alignment explanation
Indices: 978409--978443 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
978399 TTCACGAGAA
978409 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
978444 TAATAATAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.31, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:978448 original size:3 final size:3
Alignment explanation
Indices: 978442--978477 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
978432 CAACAACAAC
978442 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
978478 TTTAATTCAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:978890 original size:9 final size:9
Alignment explanation
Indices: 978861--978894 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
978851 TTTGAATTAA
978861 TTAAATAT-
1 TTAAATATC
978869 TTAAATAATC
1 TTAAAT-ATC
978879 TTAAATATC
1 TTAAATATC
978888 TTAAATA
1 TTAAATA
978895 AAATGGAGAC
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
8 6 0.25
9 12 0.50
10 6 0.25
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (9 bp):
TTAAATATC
Found at i:979168 original size:32 final size:31
Alignment explanation
Indices: 979114--979175 Score: 81
Period size: 30 Copynumber: 2.0 Consensus size: 31
979104 TAAATTATTG
979114 TTAATATATATTTTAATAATA-TTTTAAATT
1 TTAATATATATTTTAATAATATTTTTAAATT
* *
979144 TTAATGTATATTATTTATATATATTTTTAAAT
1 TTAATATATATT-TTAATA-ATATTTTTAAAT
979176 ATTTTAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
30 11 0.41
31 5 0.19
32 3 0.11
33 8 0.30
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (31 bp):
TTAATATATATTTTAATAATATTTTTAAATT
Found at i:979426 original size:26 final size:27
Alignment explanation
Indices: 979367--979426 Score: 79
Period size: 26 Copynumber: 2.3 Consensus size: 27
979357 TGAAACTATA
* *
979367 CAAGTCAACGAGTTAGAAGAGTTAATT
1 CAAGTTAACGAGTTAAAAGAGTTAATT
*
979394 CAA-TTAACGAGTTAAAAGAGTTGATT
1 CAAGTTAACGAGTTAAAAGAGTTAATT
979420 -AAGTTAA
1 CAAGTTAA
979427 AACTATATGA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
25 2 0.07
26 24 0.83
27 3 0.10
ACGTcount: A:0.43, C:0.08, G:0.20, T:0.28
Consensus pattern (27 bp):
CAAGTTAACGAGTTAAAAGAGTTAATT
Found at i:981626 original size:10 final size:10
Alignment explanation
Indices: 981611--981656 Score: 51
Period size: 10 Copynumber: 4.6 Consensus size: 10
981601 GCAACTTAAA
981611 AATAAATATT
1 AATAAATATT
981621 AATAAAT-TT
1 AATAAATATT
981630 AATTAAATATT
1 AA-TAAATATT
981641 AAATAAA-ATT
1 -AATAAATATT
*
981651 ATTAAA
1 AATAAA
981657 ATTTTGAGGG
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
9 9 0.28
10 15 0.47
11 6 0.19
12 2 0.06
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (10 bp):
AATAAATATT
Found at i:981658 original size:21 final size:20
Alignment explanation
Indices: 981613--981656 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
981603 AACTTAAAAA
*
981613 TAAATATTAATAAATTTAAT
1 TAAATATTAATAAAATTAAT
981633 TAAATATTAAATAAAATT-AT
1 TAAATATT-AATAAAATTAAT
981653 TAAA
1 TAAA
981657 ATTTTGAGGG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 14 0.64
21 8 0.36
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
TAAATATTAATAAAATTAAT
Found at i:984000 original size:24 final size:24
Alignment explanation
Indices: 983968--984017 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
983958 CCATAAGAGA
983968 AATAATGAGGCTGAAATCAAAGTG
1 AATAATGAGGCTGAAATCAAAGTG
983992 AATAATGAGGCTGAAATCAAAGTG
1 AATAATGAGGCTGAAATCAAAGTG
984016 AA
1 AA
984018 AGTGGAAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.48, C:0.08, G:0.24, T:0.20
Consensus pattern (24 bp):
AATAATGAGGCTGAAATCAAAGTG
Found at i:984936 original size:3 final size:3
Alignment explanation
Indices: 984928--984965 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
984918 ATTGATTCGT
984928 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
984966 CTGCCAAGTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:985715 original size:15 final size:15
Alignment explanation
Indices: 985695--985724 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
985685 CTCAGGTTAA
*
985695 TTGAGTTTATATCAT
1 TTGAGTTTAGATCAT
985710 TTGAGTTTAGATCAT
1 TTGAGTTTAGATCAT
985725 CGGATTTAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.27, C:0.07, G:0.17, T:0.50
Consensus pattern (15 bp):
TTGAGTTTAGATCAT
Found at i:986588 original size:15 final size:15
Alignment explanation
Indices: 986564--986595 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
986554 TAAAAAACCA
*
986564 AAACCTAATTCAATT
1 AAACCCAATTCAATT
986579 AAACCCAATTCAATT
1 AAACCCAATTCAATT
986594 AA
1 AA
986596 TCCCTAATGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.50, C:0.22, G:0.00, T:0.28
Consensus pattern (15 bp):
AAACCCAATTCAATT
Found at i:987108 original size:15 final size:15
Alignment explanation
Indices: 987078--987120 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
987068 TGGATTTATT
*
987078 GAAAGAAAAG-AAAA
1 GAAAAAAAAGAAAAA
*
987092 GAATAAAAAGAAAAA
1 GAAAAAAAAGAAAAA
987107 GAAAAAAAATGAAA
1 GAAAAAAAA-GAAA
987121 TTTGATAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
14 8 0.33
15 12 0.50
16 4 0.17
ACGTcount: A:0.79, C:0.00, G:0.16, T:0.05
Consensus pattern (15 bp):
GAAAAAAAAGAAAAA
Found at i:988351 original size:20 final size:20
Alignment explanation
Indices: 988326--988369 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
988316 TTGAATTTTC
988326 ATGTTTTATTTTAAATATTT
1 ATGTTTTATTTTAAATATTT
*
988346 ATGTTTTATTTTAAATTTTT
1 ATGTTTTATTTTAAATATTT
988366 ATGT
1 ATGT
988370 ATTTTCTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.27, C:0.00, G:0.07, T:0.66
Consensus pattern (20 bp):
ATGTTTTATTTTAAATATTT
Found at i:988434 original size:16 final size:15
Alignment explanation
Indices: 988398--988440 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
988388 GCTTCTTTGT
*
988398 TTATTTTATATTTTA
1 TTATTTAATATTTTA
988413 TATATTTAATATTTTA
1 T-TATTTAATATTTTA
*
988429 GTTATTAAATAT
1 -TTATTTAATAT
988441 GGTATTTGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 1 0.04
16 22 0.92
17 1 0.04
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (15 bp):
TTATTTAATATTTTA
Found at i:989470 original size:20 final size:18
Alignment explanation
Indices: 989445--989500 Score: 51
Period size: 22 Copynumber: 2.9 Consensus size: 18
989435 TAAATAAAGT
989445 AAATATAAAAAATTATTGA
1 AAATATAAAAAATTATT-A
*
989464 GAAATATTTAAAAAATCATTA
1 -AAATA--TAAAAAATTATTA
989485 AAATA-AAATAAATTAT
1 AAATATAAA-AAATTAT
989501 AATGAATTCA
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
17 3 0.10
18 6 0.19
20 10 0.32
21 1 0.03
22 11 0.35
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.32
Consensus pattern (18 bp):
AAATATAAAAAATTATTA
Found at i:1000775 original size:24 final size:23
Alignment explanation
Indices: 1000735--1000780 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
1000725 TATTTCATTT
*
1000735 CTGTTTTGTTTCTTTTTGTTTCTG
1 CTGTTTTCTTTCTTTTT-TTTCTG
1000759 CTGTTTTCTTT-TATTTTTTTCT
1 CTGTTTTCTTTCT-TTTTTTTCT
1000781 TCCTATTCGA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 6 0.30
24 14 0.70
ACGTcount: A:0.02, C:0.13, G:0.11, T:0.74
Consensus pattern (23 bp):
CTGTTTTCTTTCTTTTTTTTCTG
Found at i:1001332 original size:35 final size:35
Alignment explanation
Indices: 1001286--1001404 Score: 184
Period size: 35 Copynumber: 3.4 Consensus size: 35
1001276 TGAATCTCAG
* *
1001286 CAGCTTTATTTCTTCTTCATTGCTGCCGTTTGTAA
1 CAGCTTTATTTCTTATTCATTGCTGCCGTTTGCAA
* *
1001321 CAGCTTTATTTCTTATTCATTGCTGCCATTTGCAG
1 CAGCTTTATTTCTTATTCATTGCTGCCGTTTGCAA
* *
1001356 CAGCTTTATTTTTTATTCATTGCTGCTGTTTGCAA
1 CAGCTTTATTTCTTATTCATTGCTGCCGTTTGCAA
1001391 CAGCTTTATTTCTT
1 CAGCTTTATTTCTT
1001405 CTATATTAAT
Statistics
Matches: 75, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 75 1.00
ACGTcount: A:0.16, C:0.21, G:0.13, T:0.50
Consensus pattern (35 bp):
CAGCTTTATTTCTTATTCATTGCTGCCGTTTGCAA
Done.